Legumes: Embracing the genome era

Legumes (Fabaceae, formerly Leguminosae) are a diverse, widely dis-tributed, and economically important family of annual or perennialherbaceous plants, xerophytes, and forest trees. As a steady source ofproteins, vitamins, minerals, and either lipids or starch, as well as theirability to fix nitrogen, legume grains play a major role in advancinghealth and nutrition, food security, and environmental sustainability,also providing forage for livestock and serving as cover crops to con-trol weeds and erosion. The production potential of legume crops isconstrained by several abiotic and biotic stress factors. Deploymentof molecular breeding approaches for legume improvement hasgenerally lagged behind the more successful cereal and oilseed crops.However, with the recent advances in next generation sequencingand genotyping technologies, legume genomics is advancing quiterapidly. Over the past decade, reference genome sequenceshave become available for more than 45 legume species (NCBIGenome Database; https://www.ncbi.nlm.nih.gov/genome/browse/#!/overview/Fabaceae). The application of DNA and RNA sequencingis providing considerable insights into the hidden genetic, epigeneticand structural variation underlying various complex traits for legumeimprovement. This special Issue on legume genomics, comprising ninereviews, four original research articles and a resource article,addresses some of the most important advances and applications inthe field

Converging Cylindrical Shock Waves in a Nonideal Gas With an Axial Magnetic Field

This paper analyses the propagation of converging cylindrical shock waves in a nonidealgas, in the presence of an axial magnetic field. Chester-Chisnell-Whitham’s method has beenemployed to determine the shock velocity and the other flow-variables just behind the shockin the cases, when (i) the gas is weakly ionised before and behind the shock front, (ii) the gasis strongly ionised before and behind the shock front, and (iii) nonionised gas undergoes intenseionisation as a result of the passage of the shock. The effects of the nonidealness of the gas,the conductivity of the gas, and the axial magnetic field have been investigated. It is found thatin the case (i), an increase in the value of parameter ( ) characterising the nonidealness of thegas accelerates the convergence of the shock. In the case (ii), the shock speed and pressurebehind the shock increase very fast as the axis is approached; and this increase occurs earlierif the strength of the initial magnetic field is increased. In the case (iii), for smaller values of theinitial magnetic field, the shock speed, and pressure behind the shock decrease very fast afterattaining a maximum; and for higher values of the initial magnetic field, the tendency of decreaseappears from the beginning. This shows that the magnetic field has damping effect on the shockpropagation. In the case (iii), it was also found that the growth of the shock in the initial phaseand decay in the last phase were faster when it was converging in a nonideal gas in comparisonwith that in a perfect gas. Further, it has been shown that the gas-ionising nature of the shockhas damping effect on its convergence

Selective isolation and antimicrobial activity of rare actinomycetes from mangrove sediment of Karwar

The mangrove ecosystem is a largely unexplored source for actinomycetes. Various pretreatment procedures and selective media were applied to assess the optimal conditions for the isolation of rare actinomycetes from Mangrove sediment. Pretreatment of wet-heating for 15 min at 70oC and phenol treatment of soil suspension were the most effective methods for the isolation of those microorganisms. Hair hydrolysate vitamin agar (HHVA) was the most suitable medium for the recovery of rare actinomycetes. Fifty-three rare actinomycete strains were chosen using selective isolation approaches, then morphological and chemical properties of the isolates were determined. The isolates belonged to one of the following genus, Micromonospora, Microbispora, Actinoplanes, and Actinomadura. Later Micromonospora and Actinomadura were selected for antimicrobial activity. Minimum bactericidal concentration (MBC) of ethyl acetate extract against Staphylococcus aureus were 1.20 mg/ml for Micromonospora species and 5mg/ml for Actinomadura species. Thin layer chromatography (TLC) of the ethyl acetate extracts were carried out in duplicate using Chloroform: methanol (4:1) as solvent system and Tetracycline as reference antibiotic. Under UV light they gave greenish yellow spots with Rf value 0.85 for the antimicrobial from Actinomadura species and 0.88 for that from Micromonospora species. In bioautography (using Staphylococcus auras as test organism) inhibition zones were obtained and they were associated with the yellowish green spots of the chromatogram as detected under UV light. This may indicate the same compounds were responsible for the antibacterial activity of those actinomycetes isolates. ÂÂ

Assessment of genetic diversity in blackgram [Vigna mungo (L.) Hepper] germplasm

Genetic diversity analysis was carried out with 50 black gram genotypes by using Mahalanobis D2 statistics for ten quantitative traits. All the genotypes were grouped into ten non-overlapping clusters. Cluster I was the largest with 19 genotypes, followed by cluster II with 14 genotypes, cluster III with 8 genotypes, clusters VII and IX were digenotypic, while the remaining clusters IV, V, VI, VII and X were monogenotypic. The maximum inter-cluster distance was observed between cluster VII and IX. Cluster IX had recorded high mean values for most of the traits. Selection of genotypes from these diverse clusters with high mean performance and more per cent contribution as parents in the crossing may result in superior combinations along with maximum variability in the segregating generations. Hence, crosses among the genotypes viz., LBG 623 (cluster I), LBG 787 (cluster III), DKU 87 (cluster II) and VBN 8 (cluster VII) may result in production of superior pureline varieties in black gram. Among the traits, pods/plant contributed maximum towards the total divergence

Ternary structure reveals mechanism of a membrane diacylglycerol kinase

Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The g-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergen

MEMS Microshutter Array System for James Webb Space Telescope

A complex MEMS microshutter array system has been developed at NASA Goddard Space Flight Center (GSFC) for use as a multi-object aperture array for a Near-Infrared Spectrometer (NIRSpec). The NIRSpec is one of the four major instruments carried by the James Webb Space Telescope (JWST), the next generation of space telescope after the Hubble Space Telescope retires. The microshutter arrays (MSAs) are designed for the selective transmission of light with high efficiency and high contrast. It is demonstrated in Figure 1 how a MSA is used as a multiple object selector in deep space. The MSAs empower the NIRSpec instrument simultaneously collect spectra from more than 100 targets therefore increases the instrument efficiency 100 times or more. The MSA assembly is one of three major innovations on JWST and the first major MEMS devices serving observation missions in space. The MSA system developed at NASA GSFC is assembled with four quadrant fully addressable 365x171 shutter arrays that are actuated magnetically, latched and addressed electrostatically. As shown in Figure 2, each MSA is fabricated out of a 4' silicon-on-insulator (SOI) wafer using MEMS bulk-micromachining technology. Individual shutters are close-packed silicon nitride membranes with a pixel size close to 100x200 pm (Figure 3). Shutters are patterned with a torsion flexure permitting shutters to open 90 degrees with a minimized mechanical stress concentration. In order to prevent light leak, light shields are made on to the surrounding frame of each shutter to cover the gaps between the shutters and the Game (Figure 4). Micro-ribs and sub-micron bumps are tailored on hack walls and light shields, respectively, to prevent sticktion, shown in Figures 4 and 5. JWST instruments are required to operate at cryogenic temperatures as low as 35K, though they are to be subjected to various levels of ground tests at room temperature. The shutters should therefore maintain nearly flat in the entire temperature range between 35K and 300K. Through intensive numerical simulations and experimental studies, an optically opaque and electrically conductive metal-nitride thin film was selected as a coating material deposited on the shutters with the best thermal-expansion match to silicon nitride - the shutter blade thin film material. A shutter image shown in Figure 6 was taken at room temperature, presenting shutters slightly bowing down as expected. Shutters become flat when the temperature decreases to 35K. The MSAs are then bonded to silicon substrates that are fabricated out of 6" single-silicon wafers in the thickness of 2mm. The bonding is conducted using a novel single-sided indium flip-chip bonding technology. Indium bumps fabricated on a substrate are shown in Figure 7. There are 180,000 indium bumps for bonding a flight format MSA array to its substrate. Besides a MSA, each substrate houses five customer-designed ASIC (Application Specific Integrated Circuit) multiplexer/address chips for 2-dimensional addressing, twenty capacitors, two temperature sensors, numbers of resistors and all necessary interconnects, as shown in Figure 8. Complete MSA quadrant assemblies have been successfully manufactured and fully functionally tested. The assemblies have passed a series of critical reviews required by JWST in satisfying all the design specifications. The qualification tests cover programmable 2-D addressing, life tests, optical contrast tests, and environmental tests including radiation, vibration, and acoustic tests. A 2-D addressing pattern with 'ESA' letters programmed in a MSA is shown in Figure 9. The MSAs passed 1 million cycle life tests and achieved high optical contrast over 10,000. MSA teams are now making progress in final fabrication, testing and assembly (Figure 10). The delivery of flight-format MSA system is scheduled at the end of 2008 for being integrated to the focal plane of the NIRSpec detectors

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein